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Project Description

Intro

MyVariant.Info provides simple-to-use REST web services to query/retrieve genetic variant annotation data. It’s designed with simplicity and performance emphasized. myvariant, is an easy-to-use Python wrapper to access MyVariant.Info services.

Requirements

python >=2.6 (including python3)

requests (install using “pip install requests”)

Optional dependencies

pandas (install using “pip install pandas”) is required for returning a list of variant objects as DataFrame.

Installation

Option 1
pip install myvariant
Option 2

download/extract the source code and run:

python setup.py install
Option 3

install the latest code directly from the repository:

pip install -e git+https://github.com/sulab/myvariant.py

Version history

CHANGES.txt

Tutorial

Access ClinVar Data from MyVariant.info Services (the raw ipynb file is here)

TODO

Usage

In [1]: import myvariant

In [2]: mv = myvariant.MyVariantInfo()

In [3]: mv.getvariant("chr7:g.140453134T>C")
Out[3]:  #output below is collapsed
{"_id": "chr7:g.140453134T>C",
 "_version": 1,
 "cadd": {...},
 "cosmic": {...},
 "dbnsfp": {...},
 "dbsnp": {...},
 "docm": {...},
 "mutdb": {...},
 "snpeff": {...},
 "vcf": {
    "alt": "C",
    "position": "140453134",
    "ref": "T"
 }}

In [4]: mv.getvariant("chr7:g.140453134T>C", fields='cosmic,snpeff')
Out[4]:
{'_id': 'chr7:g.140453134T>C',
 '_version': 1,
 'snpeff': {'ann': {'transcript_biotype': 'Coding',
   'gene_id': 'BRAF',
   'effect': 'missense_variant',
   'putative_impact': 'MODERATE',
   'cds': {'length': '2301', 'position': '1801'},
   'feature_type': 'transcript',
   'gene_name': 'BRAF',
   'feature_id': 'NM_004333.4',
   'hgvs_p': 'p.Lys601Glu',
   'hgvs_c': 'c.1801A>G',
   'rank': '15',
   'total': '18',
   'protein': {'length': '766', 'position': '601'},
   'cdna': {'length': '2946', 'position': '1862'}}},
 'cosmic': {'mut_freq': 0.07,
  'alt': 'G',
  'mut_nt': 'A>G',
  'tumor_site': 'upper_aerodigestive_tract',
  'ref': 'A',
  'chrom': '7',
  'hg19': {'start': 140453134, 'end': 140453134},
  'cosmic_id': 'COSM478'}
 }

In [5]: mv.getvariant("chr7:g.140453134T>C", fields=['cosmic.tumor_site', 'snpeff.ann.gene_name'])
Out[5]:
{'_id': 'chr7:g.140453134T>C',
 '_version': 1,
 'snpeff': {'ann': {'gene_name': 'BRAF'}},
 'cosmic': {'tumor_site': 'upper_aerodigestive_tract'}
}

In [6]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'])
Out[6]:
[{'_id': 'chr1:g.866422C>T',
   ...
 },
 {'_id': 'chr1:g.876664G>A',
  ...
 },
 {'_id': 'chr1:g.69635G>C',
  ...
 }]

In [7]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'],
fields='cadd.phred,dbsnp.rsid')
Out[7]:
[{'query': 'chr1:g.866422C>T',
  '_id': 'chr1:g.866422C>T',
  'dbsnp': {'rsid': 'rs139210662'},
  'cadd': {'phred': 14.31}},
 {'query': 'chr1:g.876664G>A',
  '_id': 'chr1:g.876664G>A',
  'dbsnp': {'rsid': 'rs571654307'},
  'cadd': {'phred': 9.971}},
 {'query': 'chr1:g.69635G>C',
  '_id': 'chr1:g.69635G>C',
  'dbsnp': {'rsid': 'rs541766448'},
  'cadd': {'phred': 6.123}}]

In [8]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'],
fields='cadd.phred,dbsnp.rsid', as_dataframe=True)
Out[8]:
                               _id  cadd.phred   dbsnp.rsid
query
chr1:g.866422C>T  chr1:g.866422C>T      14.310  rs139210662
chr1:g.876664G>A  chr1:g.876664G>A       9.971  rs571654307
chr1:g.69635G>C    chr1:g.69635G>C       6.123  rs541766448

In [9]: mv.query('dbsnp.rsid:rs58991260', fields='dbsnp')
Out[9]:
{'total': 1,
 'hits': [{'_score': 17.48471,
   '_id': 'chr1:g.218631822G>A',
   'dbsnp': {'class': 'SNV',
    'gmaf': 0.02157,
    'vartype': 'snp',
    'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],
    'var_subtype': 'ts',
    'alleles': [{'freq': 0.9784, 'allele': 'G'},
     {'freq': 0.02157, 'allele': 'A'}],
    'allele_origin': 'unspecified',
    'chrom': '1',
    'hg19': {'start': 218631822, 'end': 218631823},
    'validated': True,
    'dbsnp_build': 129,
    'alt': 'A',
    'rsid': 'rs58991260',
    'ref': 'G'}}],
 'took': 24,
 'max_score': 17.48471}


In [10]: mv.query('snpeff.ann.gene_name:cdk2 AND dbnsfp.polyphen2.hdiv.pred:D',
fields='dbnsfp.polyphen2.hdiv')
Out[10]:
{'total': 1188,
 'hits': [{'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,
      'pred': 'D',
      'score': 1.0}}},
   '_score': 8.343648,
   '_id': 'chr12:g.56359720C>T'},
  {'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,
      'pred': 'D',
      'score': [1.0, 0.957, 0.998]}}},
   '_score': 8.343648,
   '_id': 'chr12:g.56360819G>C'},

   ...

  {'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,
      'pred': 'D',
      'score': 1.0}}},
   '_score': 8.343648,
   '_id': 'chr12:g.56360853G>A'}],
   'took': 3521,
   'max_score': 8.343648}


In [11]: mv.query('chr1:69000-70000', fields='cadd.phred')
Out[11]:
{'total': 3,
 'hits': [
  {'_score': 14.155852, '_id': 'chr1:g.69428T>G', 'cadd': {'phred': 12.14}},
  {'_score': 14.148425, '_id': 'chr1:g.69511A>G', 'cadd': {'phred': 8.98}},
  {'_score': 3.5420983, '_id': 'chr1:g.69538G>A', 'cadd': {'phred': 7.339}}],
 'took': 725,
 'max_score': 14.155852}

In [12]: mv.querymany(['rs58991260', 'rs2500'], scopes='dbsnp.rsid', fields='dbsnp')
Finished.
Out[12]:
[{'query': 'rs58991260',
  '_id': 'chr1:g.218631822G>A',
  'dbsnp': {'class': 'SNV',
   'gmaf': 0.02157,
   'vartype': 'snp',
   'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],
   'var_subtype': 'ts',
   'alleles': [{'freq': 0.9784, 'allele': 'G'},
    {'freq': 0.02157, 'allele': 'A'}],
   'allele_origin': 'unspecified',
   'chrom': '1',
   'hg19': {'start': 218631822, 'end': 218631823},
   'validated': True,
   'dbsnp_build': 129,
   'alt': 'A',
   'rsid': 'rs58991260',
   'ref': 'G'}},
 {'query': 'rs2500',
  '_id': 'chr11:g.66397320A>G',
  'dbsnp': {'class': 'SNV',
   'vartype': 'snp',
   'flags': ['ASP', 'INT', 'RV', 'U3'],
   'var_subtype': 'ts',
   'alleles': [{'allele': 'A'}, {'allele': 'G'}],
   'allele_origin': 'unspecified',
   'chrom': '11',
   'hg19': {'start': 66397320, 'end': 66397321},
   'dbsnp_build': 36,
   'alt': 'G',
   'ref': 'A',
   'rsid': 'rs2500',
   'validated': False}}]

In [13]: mv.querymany(['RCV000083620', 'RCV000083584'],
scopes='clinvar.rcv_accession', fields='clinvar')
Finished.
Out[13]:
[{'query': 'RCV000083620',
  'clinvar': {'type': 'single nucleotide variant',
   'gene': {'id': 5009, 'symbol': 'OTC'},
   'origin': 'unknown',
   'last_evaluated': 'None',
   'other_ids': 'dbSNP:72558473;',
   'clinvar_id': 97371,
   'hgvs': {'genomic': ['NG_008471.1:g.64470C>T',
     'NC_000023.11:g.38411952C>T',
     'NC_000023.10:g.38271205C>T'],
    'coding': 'NM_000531.5:c.958C>T'},
   'chrom': 'X',
   'cytogenic': 'Xp11.4',
   'name': 'NM_000531.5(OTC):c.958C>T (p.Arg320Ter)',
   'number_submitters': 1,
   'alt': 'T',
   'hg19': {'start': 38271205, 'end': 38271205},
   'allele_id': 103263,
   'rcv_accession': 'RCV000083620',
   'review_status': 'classified by single submitter',
   'clinical_significance': 'Pathogenic',
   'rsid': 'rs72558473',
   'ref': 'C'},
  '_id': 'chrX:g.38271205C>T'},
 {'query': 'RCV000083584',
  'clinvar': {'type': 'Deletion',
   'gene': {'id': 5009, 'symbol': 'OTC'},
   'origin': 'unknown',
   'last_evaluated': 'None',
   'other_ids': 'dbSNP:72558452;',
   'clinvar_id': 97337,
   'hgvs': {'genomic': ['NG_008471.1:g.61493_61495delGAG',
     'NC_000023.11:g.38408975_38408977delGAG',
     'NC_000023.10:g.38268228_38268230delGAG'],
    'coding': 'NM_000531.5:c.817_819delGAG'},
   'chrom': 'X',
   'cytogenic': 'Xp11.4',
   'name': 'NM_000531.5(OTC):c.817_819delGAG (p.Glu273del)',
   'number_submitters': 1,
   'alt': '-',
   'hg19': {'start': 38268228, 'end': 38268230},
   'allele_id': 103229,
   'rcv_accession': 'RCV000083584',
   'review_status': 'classified by single submitter',
   'clinical_significance': 'Pathogenic',
   'rsid': 'rs72558452',
   'ref': 'GAG'},
  '_id': 'chrX:g.38268228_38268230del'}]

In [14]: mv.querymany(['rs2500', 'RCV000083611', 'COSM1392449'],
scopes='clinvar.rcv_accession,dbsnp.rsid,cosmic.cosmic_id', fields='vcf', as_dataframe=1)
Finished.
Out[14]:
                              _id vcf.alt vcf.position vcf.ref
query
rs2500        chr11:g.66397320A>G       G     66397320       A
RCV000083611   chrX:g.38271176A>G       G     38271176       A
COSM1392449   chr19:g.30935013C>T       T     30935013       C


In [15]: mv.querymany(['rs58991260', 'rs2500', 'NA_TEST'], scopes='dbsnp.rsid', fields='dbsnp')
Finished.
1 input query terms found no hit:
        ['NA_TEST']
Pass "returnall=True" to return complete lists of duplicate or missing query terms.
Out[15]:
[{'query': 'rs58991260',
  '_id': 'chr1:g.218631822G>A',
  'dbsnp': {'class': 'SNV',
   'gmaf': 0.02157,
   'vartype': 'snp',
   'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],
   'var_subtype': 'ts',
   'alleles': [{'freq': 0.9784, 'allele': 'G'},
    {'freq': 0.02157, 'allele': 'A'}],
   'allele_origin': 'unspecified',
   'chrom': '1',
   'hg19': {'start': 218631822, 'end': 218631823},
   'validated': True,
   'dbsnp_build': 129,
   'alt': 'A',
   'rsid': 'rs58991260',
   'ref': 'G'}},
 {'query': 'rs2500',
  '_id': 'chr11:g.66397320A>G',
  'dbsnp': {'class': 'SNV',
   'vartype': 'snp',
   'flags': ['ASP', 'INT', 'RV', 'U3'],
   'var_subtype': 'ts',
   'alleles': [{'allele': 'A'}, {'allele': 'G'}],
   'allele_origin': 'unspecified',
   'chrom': '11',
   'hg19': {'start': 66397320, 'end': 66397321},
   'dbsnp_build': 36,
   'alt': 'G',
   'ref': 'A',
   'rsid': 'rs2500',
   'validated': False}},
 {'query': 'NA_TEST', 'notfound': True}]

Contact

Drop us any feedback at: help@myvariant.info or on twitter @myvariantinfo.

Release History

Release History

0.3.1

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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0.3.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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0.2.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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0.1.2

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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0.1.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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0.1.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
myvariant-0.3.1-py2.py3-none-any.whl (16.6 kB) Copy SHA256 Checksum SHA256 3.5 Wheel Aug 19, 2016
myvariant-0.3.1.tar.gz (16.2 kB) Copy SHA256 Checksum SHA256 Source Aug 19, 2016

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